Search · four archives
Search · four archives
11 papers · ranked by Valyu relevance
Authors not listed
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high…
Pierre Carrier, Bill Long, Richard Walsh, Jef Dawson + 4 more
High Performance Computing (HPC) Best Practice offers opportunities to implement lessons learned in areas such as computational chemistry and physics in genomics workflows, specifically Next-Generation Sequencing (NGS) workflows. In this study we will briefly describe how distributed-memory parallelism can be an…
Authors not listed
Machine learning models are transforming data-driven research across scientific disciplines, yet their deployment as accessible and reliable web services remains a significant challenge. We introduce the NERDD framework, a scalable, maintainable, and secure microservices platform designed to support the sustainable…
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri + 3 more
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
Federico Marotta, Oliver Stolpe, Benedikt Obermayer, January Weiner + 3 more
In many bioinformatic data analysis projects, it is convenient to visualize plots and results through an interactive web app or dashboard. These interactive reports can then be shared with customers, collaborators, or the general public. Publishing and sharing these apps is not straightforward, becoming especially…
Lester Melie-Garcia, Bogdan Draganski, John Ashburner, Ferath Kherif
We propose a Multiple Linear Regression (MLR) methodology for the analysis of distributed and Big Data in the framework of the Medical Informatics Platform (MIP) of the Human Brain Project (HBP). MLR is a very versatile model, and is considered one of the workhorses for estimating dependences between clinical…
Azza E Ahmed, Joshua M Allen, Tajesvi Bhat, Prakruthi Burra + 16 more
The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software…
Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis + 9 more
Computer simulation is an indispensable tool for studying complex biological systems. In particular, agent-based modeling is an attractive method to describe biophysical dynamics. However, two barriers limit faster progress. First, simulators do not always take full advantage of parallel and heterogeneous hardware.…
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
Authors not listed
Self-driving laboratories (SDLs) promise accelerated scientific discovery and product development by closing the loop between robotic execution and AI/ML-driven decision making. In practice, however, SDL orchestration remains fragmented; workflows are typically encoded as laboratory-specific scripts or bespoke…